API for immunarch
Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design in R
| Global functions | |
|---|---|
| .as_tsv | Source code |
| .check_empty_repertoires | Source code |
| .colourblind_discrete | Source code |
| .colourblind_vector | Source code |
| .detect_format | Source code |
| .get_coltypes | Source code |
| .im_ns | Source code |
| .make_names | Source code |
| .onAttach | Source code |
| .onLoad | Source code |
| .postprocess | Source code |
| .quant_column_choice | Man page Source code |
| .rem_legend | Source code |
| .rem_xlab | Source code |
| .rem_ylab | Source code |
| .remove.alleles | Source code |
| .remove.ext | Source code |
| .rlang_purrr_args_recycle | Source code |
| .rlang_purrr_index | Source code |
| .rlang_purrr_map_mold | Source code |
| .rlang_purrr_probe | Source code |
| .tweak_col | Source code |
| .tweak_fill | Source code |
| .validate_immdata | Source code |
| .validate_repertoires_data | Source code |
| .which_recomb_type | Source code |
| AA_PROP | Man page |
| AA_TABLE | Man page |
| AA_TABLE_REVERSED | Man page |
| ATCHLEY | Man page |
| GENE_SEGMENTS | Man page |
| KIDERA | Man page |
| aa_prop | Man page |
| aa_properties | Man page |
| aa_table | Man page |
| accumulate | Source code |
| accumulate_right | Source code |
| add_class | Man page Source code |
| add_column_with_first_gene | Source code |
| add_column_without_alleles | Source code |
| add_empty_columns | Source code |
| add_pb | Man page Source code |
| airr_clonality | Man page |
| airr_clonality_line | Man page |
| airr_clonality_line_impl | Source code |
| airr_clonality_prop | Man page |
| airr_clonality_prop_impl | Source code |
| airr_clonality_rank | Man page |
| airr_clonality_rank_impl | Source code |
| airr_diversity | Man page |
| airr_diversity_chao1 | Man page |
| airr_diversity_chao1_impl | Source code |
| airr_diversity_dxx | Man page |
| airr_diversity_dxx_impl | Source code |
| airr_diversity_hill | Man page |
| airr_diversity_hill_impl | Source code |
| airr_diversity_index | Man page |
| airr_diversity_index_impl | Source code |
| airr_diversity_pielou | Man page |
| airr_diversity_pielou_impl | Source code |
| airr_diversity_shannon | Man page |
| airr_diversity_shannon_impl | Source code |
| airr_public | Man page |
| airr_public_intersection | Man page |
| airr_public_intersection_impl | Source code |
| airr_public_jaccard | Man page |
| airr_public_jaccard_impl | Source code |
| airr_stats | Man page |
| airr_stats_chains | Man page |
| airr_stats_chains_impl | Source code |
| airr_stats_genes | Man page |
| airr_stats_genes_impl | Source code |
| airr_stats_lengths | Man page |
| airr_stats_lengths_impl | Source code |
| align_single_df | Source code |
| annotate_clonality | Man page |
| annotate_clonality_prop | Man page |
| annotate_clonality_prop_impl | Source code |
| annotate_clonality_rank | Man page |
| annotate_clonality_rank_impl | Source code |
| apply_asymm | Man page Source code |
| apply_symm | Man page Source code |
| apply_to_sample_or_list | Source code |
| as_numeric_or_fail | Source code |
| atchley | Man page |
| base_clonality_prop | Source code |
| base_clonality_rank | Source code |
| bcrdata | Man page |
| bunch_translate | Man page Source code |
| calculate_germlines_parallel | Source code |
| chao1 | Man page Source code |
| check_distribution | Man page Source code |
| check_group_names | Source code |
| clonal.prop | Man page |
| clonal_proportion | Man page Source code |
| clonal_space_homeostasis | Man page Source code |
| clonality | Man page |
| coding | Man page Source code |
| compact | Source code |
| convert_nested_to_df | Source code |
| convert_results_to_df | Source code |
| convert_seq_list_to_dnabin | Source code |
| cosine_sim | Source code |
| cosine_sim.default | Source code |
| cosine_sim.numeric | Source code |
| cross_entropy | Man page Source code |
| dXX | Source code |
| dbAnnotate | Man page Source code |
| dbLoad | Man page Source code |
| default_scale_fun | Source code |
| detect | Source code |
| detect_index | Source code |
| discard | Source code |
| diversity_eco | Man page Source code |
| downsample | Source code |
| downsample_col | Source code |
| entropy | Man page Source code |
| every | Source code |
| exclude | Man page Source code |
| fill_missing_columns | Source code |
| fill_reads | Source code |
| fill_vec | Source code |
| filter_by_clonotype | Source code |
| filter_by_meta | Source code |
| filter_by_repertoire | Source code |
| filter_table | Source code |
| fixVis | Man page Source code |
| geneUsage | Man page Source code |
| geneUsageAnalysis | Man page Source code |
| gene_segments | Man page |
| gene_stats | Man page Source code |
| gene_usage_cor | Source code |
| gene_usage_cosine | Source code |
| gene_usage_js | Source code |
| genes | Man page |
| germline_single_df | Source code |
| get.kmers | Man page |
| getKmers | Man page Source code |
| get_airr_method | Source code |
| get_aliases | Man page |
| get_empty_object_with_class | Source code |
| get_genes | Man page Source code |
| get_immunarch_news | Man page Source code |
| get_public_repertoire_names | Source code |
| gini_coef | Man page Source code |
| gini_simpson | Man page Source code |
| group_by_colnames | Source code |
| group_from_metadata | Man page Source code |
| has_class | Man page Source code |
| has_no_data | Source code |
| hill_numbers | Man page Source code |
| horn_index | Source code |
| im_as_result | Source code |
| im_common_args | Man page Source code |
| im_ensure_vis_s3_for | Source code |
| im_method | Source code |
| im_norm | Source code |
| im_result_class | Source code |
| im_vis_s3_exists | Source code |
| imap | Source code |
| immdata | Man page |
| immunarch_data_format | Man page |
| immunarch_methods | Source code |
| immunarch_v1_update_oct_2025 | Source code |
| immunarch_v1_updates | Man page |
| immunr_data_format | Man page |
| immunr_dbscan | Man page Source code |
| immunr_hclust | Man page Source code |
| immunr_kmeans | Man page Source code |
| immunr_mds | Man page Source code |
| immunr_pca | Man page Source code |
| immunr_tsne | Man page Source code |
| inc_overlap | Man page Source code |
| include | Man page Source code |
| inframes | Man page Source code |
| interval | Man page Source code |
| inverse_simpson | Man page Source code |
| jaccard_index | Source code |
| jaccard_index.character | Source code |
| jaccard_index.default | Source code |
| js_div | Man page Source code |
| keep | Source code |
| kidera | Man page |
| kl_div | Man page Source code |
| kmer_profile | Man page Source code |
| lessthan | Man page Source code |
| list_c | Source code |
| list_immunarch_news | Man page Source code |
| load_segments | Source code |
| makeKmerTable | Man page |
| make_airr_dispatcher | Source code |
| make_dotplot | Source code |
| make_dynam_col_plot | Source code |
| make_fixed_col_plot | Source code |
| make_immunarch_features | Source code |
| make_immunarch_method_record | Source code |
| map | Source code |
| map2 | Source code |
| map2_chr | Source code |
| map2_dbl | Source code |
| map2_int | Source code |
| map2_lgl | Source code |
| map_chr | Source code |
| map_dbl | Source code |
| map_if | Source code |
| map_int | Source code |
| map_lgl | Source code |
| matrixdiagcopy | Man page Source code |
| morethan | Man page Source code |
| morisita_index | Source code |
| negate | Source code |
| noncoding | Man page Source code |
| num2bin | Source code |
| num_shared_clonotypes | Source code |
| optional_sample | Source code |
| outofframes | Man page Source code |
| overlap_coef | Source code |
| overlap_coef.character | Source code |
| overlap_coef.default | Source code |
| par_or_normal_apply | Source code |
| par_or_normal_lapply | Source code |
| parse_10x_consensus | Source code |
| parse_10x_filt_contigs | Source code |
| parse_airr | Source code |
| parse_archer | Source code |
| parse_catt | Source code |
| parse_imgt | Source code |
| parse_immunarch | Source code |
| parse_immunoseq | Source code |
| parse_imseq | Source code |
| parse_migec | Source code |
| parse_migmap | Source code |
| parse_mitcr | Source code |
| parse_mixcr | Source code |
| parse_repertoire | Source code |
| parse_rtcr | Source code |
| parse_tcr | Source code |
| parse_vdjtools | Source code |
| pmap | Source code |
| prepare_results_row | Source code |
| process_cluster | Source code |
| process_col_argument | Man page Source code |
| process_dataframe | Source code |
| process_metadata_arguments | Source code |
| properties | Man page |
| pubRep | Man page Source code |
| pubRepApply | Man page Source code |
| pubRepFilter | Man page Source code |
| pubRepStatistics | Man page Source code |
| publicRepertoire | Man page |
| publicRepertoireApply | Man page |
| publicRepertoireFilter | Man page |
| public_matrix | Man page Source code |
| quiet | Source code |
| rare_proportion | Man page Source code |
| rarefaction | Man page Source code |
| reduce | Source code |
| reduce_right | Source code |
| register_airr_family | Source code |
| register_airr_method | Source code |
| register_immunarch_method | Man page Source code |
| register_immunarch_visualisation | Source code |
| rename_column | Source code |
| repAlignLineage | Man page Source code |
| repClonalFamily | Man page Source code |
| repClonality | Man page Source code |
| repDiversity | Man page Source code |
| repExplore | Man page Source code |
| repFilter | Man page Source code |
| repGermline | Man page Source code |
| repLoad | Man page Source code |
| repOverlap | Man page Source code |
| repOverlapAnalysis | Man page Source code |
| repSample | Man page Source code |
| repSave | Man page |
| repSomaticHypermutation | Man page Source code |
| require_system_package | Source code |
| resample | Source code |
| resample_col | Source code |
| return_families | Source code |
| return_segments | Source code |
| rotate_x_text | Source code |
| sample_clonotypes | Source code |
| save_immunarch | Source code |
| save_vdjtools | Source code |
| segments | Man page |
| select_barcodes | Man page Source code |
| select_clusters | Man page |
| seqCluster | Man page Source code |
| seqDist | Man page Source code |
| set_pb | Man page Source code |
| shm_process_clonotype_row | Source code |
| shm_process_dataframe | Source code |
| some | Source code |
| sort_string | Source code |
| spectratype | Man page Source code |
| split_to_kmers | Man page Source code |
| startswith_rows | Source code |
| substring_rows | Source code |
| switch_type | Man page Source code |
| theme_cleveland2 | Source code |
| theme_pubr | Source code |
| top | Man page Source code |
| top_proportion | Man page Source code |
| trackClonotypes | Man page Source code |
| translate_bunch | Man page |
| transpose | Source code |
| tversky_index | Source code |
| tversky_index.character | Source code |
| tversky_index.default | Source code |
| validate_columns | Source code |
| vis | Man page Source code |
| vis.clonal_family | Man page Source code |
| vis.clonal_family_tree | Man page Source code |
| vis.immunr_chao1 | Man page Source code |
| vis.immunr_clonal_prop | Man page Source code |
| vis.immunr_dbscan | Man page Source code |
| vis.immunr_div | Man page Source code |
| vis.immunr_dxx | Man page Source code |
| vis.immunr_dynamics | Man page Source code |
| vis.immunr_exp_clones | Man page Source code |
| vis.immunr_exp_count | Man page Source code |
| vis.immunr_exp_len | Man page Source code |
| vis.immunr_exp_vol | Man page Source code |
| vis.immunr_gene_usage | Man page Source code |
| vis.immunr_ginisimp | Man page Source code |
| vis.immunr_gu_matrix | Man page Source code |
| vis.immunr_hclust | Man page Source code |
| vis.immunr_hill | Man page Source code |
| vis.immunr_homeo | Man page Source code |
| vis.immunr_inc_overlap | Man page Source code |
| vis.immunr_invsimp | Man page Source code |
| vis.immunr_kmeans | Man page Source code |
| vis.immunr_kmer_profile_pfm | Source code |
| vis.immunr_kmer_profile_ppm | Source code |
| vis.immunr_kmer_profile_pwm | Source code |
| vis.immunr_kmer_profile_self | Source code |
| vis.immunr_kmer_table | Man page Source code |
| vis.immunr_mds | Man page Source code |
| vis.immunr_ov_matrix | Man page Source code |
| vis.immunr_pca | Man page Source code |
| vis.immunr_public_repertoire | Man page Source code |
| vis.immunr_public_statistics | Man page Source code |
| vis.immunr_rare_prop | Source code |
| vis.immunr_rarefaction | Man page Source code |
| vis.immunr_spectr | Source code |
| vis.immunr_spectr_nogene | Source code |
| vis.immunr_tail_prop | Man page |
| vis.immunr_top_prop | Man page Source code |
| vis.immunr_tsne | Man page Source code |
| vis.step_failure_ignored | Man page Source code |
| vis_bar | Man page Source code |
| vis_bar_stacked | Source code |
| vis_box | Man page Source code |
| vis_circos | Man page Source code |
| vis_heatmap | Man page Source code |
| vis_heatmap2 | Man page Source code |
| vis_hist | Man page Source code |
| vis_immunr_kmer_profile_main | Man page Source code |
| vis_public_clonotypes | Man page Source code |
| vis_public_frequencies | Man page Source code |
| vis_seqlogo | Man page Source code |
| vis_textlogo | Man page Source code |
| walk | Source code |
